Contacts of the strand formed by residues 83 - 92 (chain A) in PDB entry 1SNG
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LEU 83 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A VAL* 3.7 40.2 - - + +
80A SER* 3.3 29.1 + - - +
82A ASP* 1.3 80.5 - - - +
84A ALA* 1.3 63.0 + - - +
85A SER* 3.7 16.6 - - - +
138A ARG* 3.2 20.4 + - - -
162A LEU* 3.6 31.9 - - + -
163A TRP* 3.5 5.4 - - - +
164A ALA* 4.5 8.1 - - + -
353A LEU* 3.8 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A LEU* 1.3 75.0 - - - +
85A SER* 1.3 58.5 + - - +
136A ALA 3.5 20.9 - - - +
137A THR* 3.8 19.4 - - - +
138A ARG* 4.3 11.7 - - - +
161A ALA 4.0 0.3 - - - +
162A LEU* 3.4 5.9 - - - +
163A TRP* 2.9 54.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A TYR* 4.2 7.7 + - - -
38A SER* 5.0 0.5 + - - -
41A CAF 4.2 20.6 - - - +
77A VAL* 5.4 4.0 - - - -
83A LEU* 3.7 20.1 - - - +
84A ALA* 1.3 74.5 - - - +
86A ARG* 1.3 66.9 + - - +
109A PRO* 4.6 6.8 + - - -
110A ASP* 3.3 30.6 + - - +
136A ALA* 4.5 7.6 + - - +
137A THR* 5.4 0.7 - - - -
160A ASN* 4.8 1.2 + - - -
161A ALA 3.6 7.0 + - - -
162A LEU* 3.7 8.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A SER* 1.3 77.9 + - - +
87A THR* 1.3 63.5 + - - +
88A VAL* 3.5 19.0 - - + +
110A ASP* 3.5 30.7 + - - +
111A SER 4.2 2.4 + - - +
112A ASP* 4.1 21.7 + - - +
114A ARG* 4.4 8.5 - - - +
132A ASP* 3.0 33.4 + - - +
133A ILE* 3.7 23.6 - - + +
136A ALA* 3.6 30.1 - - + +
137A THR* 4.9 6.9 - - + +
159A THR 4.0 0.2 - - - +
160A ASN* 3.2 6.3 + - - -
161A ALA 2.9 34.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A CAF 3.2 30.4 + - - +
42A ALA* 5.0 1.8 - - + -
86A ARG* 1.3 72.1 + - - +
88A VAL* 1.3 72.0 + - - +
105A MET* 4.4 12.6 - - - -
110A ASP 3.2 7.1 + - - +
111A SER* 3.2 12.7 + - - -
112A ASP 3.0 23.0 + - - -
158A LEU* 3.9 31.9 - - + -
159A THR 3.4 4.3 - - - +
160A ASN* 2.6 26.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A ARG* 3.5 21.5 - - + +
87A THR* 1.3 85.7 - - - +
89A LEU* 1.3 70.3 + - - +
90A TRP* 3.4 38.1 - - + +
112A ASP* 3.2 9.9 - - + +
114A ARG* 3.8 17.5 - - + -
132A ASP* 3.2 28.5 - - - +
158A LEU* 3.5 1.9 - - - -
159A THR* 2.9 37.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A LEU* 4.6 9.0 - - + -
88A VAL* 1.3 71.2 - - - +
90A TRP* 1.3 58.7 + - - +
91A VAL* 3.8 20.4 - - + -
101A PHE* 3.6 31.9 - - + -
105A MET* 3.9 18.6 - - + +
112A ASP 3.1 8.4 + - - +
113A VAL* 3.4 10.1 - - + +
114A ARG 2.9 24.9 + - - +
156A ALA* 4.6 11.0 - - + -
157A ILE 3.6 25.8 - - - +
158A LEU* 4.0 17.7 - - + +
289A ILE* 4.4 14.8 - - + -
294A LEU* 5.8 0.7 - - + -
296A VAL* 4.9 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A VAL* 3.4 23.0 - - + +
89A LEU* 1.3 70.7 - - - +
91A VAL* 1.3 59.8 + - - +
114A ARG* 3.4 62.8 - - + -
115A THR 4.3 5.8 - - - -
116A ALA* 4.2 16.8 - - + -
118A PHE* 3.8 13.8 - - + -
125A VAL* 5.6 0.2 - - + -
128A THR* 3.9 21.1 - - + -
129A VAL* 3.5 39.2 - - + +
132A ASP* 3.9 17.5 + - + -
156A ALA* 3.2 4.9 - - - -
157A ILE* 2.8 48.6 + - + +
159A THR* 3.0 34.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A LEU* 3.8 34.8 - - + +
90A TRP* 1.3 77.9 - - - +
92A SER* 1.3 71.3 + - - +
95A VAL* 3.6 37.2 - - + +
97A VAL* 4.1 13.5 - - + -
113A VAL* 4.1 12.1 - - + -
114A ARG 2.8 9.4 + - - +
115A THR* 3.3 6.8 + - - +
116A ALA 2.9 19.8 + - - +
118A PHE* 3.9 4.3 - - - -
155A ARG 3.3 10.8 - - - +
156A ALA* 4.8 2.7 - - + -
294A LEU* 4.8 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A VAL* 1.3 76.6 - - - +
93A ALA* 1.3 64.4 + - - +
94A ASP* 3.3 23.9 + - - +
95A VAL* 3.0 28.1 + - - +
115A THR* 4.7 0.9 + - - +
116A ALA 3.3 10.4 + - - -
117A ASP* 5.8 0.2 - - - -
118A PHE* 3.7 9.6 + - - +
119A ARG* 6.2 0.3 - - - +
154A LEU 4.4 1.3 - - - -
155A ARG* 2.9 39.4 + - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il